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FSPAM:A Feature Construction Method to Identifying Cell Populations in ScRNA-seq Data

Computer Modeling in Engineering & Sciences 2020年第1期122卷 377-397页

作者： Amin Einipour Mohammad Mosleh Karim Ansari-asl Department of Computer Engineering Dezful BranchIslamic Azad UniversityDezfulIran Department of Electrical Engineering Faculty of EngineeringShahid Chamran University of AhvazAhvazIran

The emergence of single-cell RNA-sequencing(scRNA-seq)technology has introduced new information about the structure of cells,diseases,and their associated biological *** of the main uses of scRNA-seq is identifying cell populations,which sometimes leads to the detection of rare cell ***,the new method is still in its infancy and with its advantages comes computational challenges that are just beginning to *** important tool in the analysis is dimensionality reduction,which transforms high dimensional data into a meaningful reduced *** technique allows noise removal,visualization and compression of high-dimensional *** paper presents a new dimensionality reduction approach where,during an unsupervised multistage process,a feature set including high valuable markers is created which can facilitate the isolation of cell *** proposed method,called fusion of the Spearman and Pearson affinity matrices(FSPAM),is based on a graph-based Gaussian *** of the graph theory can be effective to overcome the challenge of the nonlinear relations between cellular markers in scRNA-seq ***,with a proper fusion of the Pearson and Spearman correlation coefficient criteria,it extracts a set of the most important features in a new *** fact,the FSPAM aggregates the various aspects of cell-to-cell similarity derived from the Pearson and Spearman metrics,and reveals new aspects of cell-to-cell similarity,which can be used to extract new *** results of the identification of cell populations via k-means++clustering method based on the features extracted from the FSPAM and different datasets of scRNA-seq suggested that the proposed method,regardless of the characteristics that govern each dataset,enjoys greater accuracy and better quality compared to previous methods.

关键词： Single cell RNA sequencing cell population feature extraction fusion

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Problems of Lifts in Symplectic Geometry

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Chinese Annals of Mathematics,Series B 2019年第3期40卷 321-330页

作者： Arif SALIMOV Manouchehr BEHBOUDI asl Sevil KAZIMOVA Department of Algebra and Geometry Baku State University Department of Mathematics Salmas Branch Islamic Azad University

Let(M,ω)be a symplectic *** this paper,the authors consider the notions of musical(bemolle and diesis)isomorphisms ω~b:T M→T~*M and ω~?:T~*M→TM between tangent and cotangent *** authors prove that the complete lifts of symplectic vector field to tangent and cotangent bundles is ω~*** consequence of analyze of connections between the complete lift ~cω_(T M )of symplectic 2-form ω to tangent bundle and the natural symplectic 2-form dp on cotangent bundle,the authors proved that dp is a pullback o f^cω_(TM)by ω~?.Also,the authors investigate the complete lift ~cφ_T~*_M )of almost complex structure φ to cotangent bundle and prove that it is a transform by ω~?of complete lift^cφ_(T M )to tangent bundle if the triple(M,ω,φ)is an almost holomorphic *** transform of complete lifts of vector-valued 2-form is also studied.

关键词： Symplectic manifold Tangent bundle Cotangent bundle Transform of tensor fields Pullback Pure tensor Holomorphic manifold

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GenFloor:Interactive generative space layout system via encoded tree graphs

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Frontiers of Architectural Research 2021年第4期10卷 771-786页

作者： Mohammad Keshavarzi Mohammad Rahmani-asl Department of Architecture University of CaliforniaBerkeleyCAUSA Autodesk Inc. San FranciscoCAUSA

Automated floorplanning or space layout planning has been a long-standing NP-hard problem in the field of computer-aided design,with applications in integrated circuits,architecture,urbanism,and operational *** this paper,we introduce GenFloor,an interactive design system that takes geometrical,topological,and performance goals and constraints as input and provides optimized spatial design solutions as *** part of our work,we propose three novel permutation methods for existing space layout graph representations,namely O-Tree and B*-Tree *** implement our proposed floorplanning methods as a package for Dynamo,a visual programming tool,with a custom GUI and additional evaluation functionalities to facilitate designers in their generative design ***,we illustrate the performance of GenFloor in two sets of case-study experiments for residential floorplanning tasks by(a)measuring the ability of the proposed system to find a known optimal solution,and(b)observing how the system can generate diverse floorplans while addressing given a constant residential design *** results indicate that convergence to the global optimum is achieved while offering a diverse set of solutions of a residential floorplan corresponding to local optimums of the solution landscape.

关键词： Generative design Floorplanning Optimization Space layout Performance-based design Optioneering

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Regulation of neural stem cell fate decisions by mitochondrial dynamics

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Neural Regeneration Research 2018年第9期13卷 1548-1549页

作者： Matthew Laaper Arezu Jahani-asl Lady Davis Institute for Medical Research Jewish General Hospital Integrated Program in Neuroscience Mc Gill University Department of Oncology Faculty of MedicineMc Gill University Division of Experimental Medicine McGill University

Stem cells possess the ability to divide symmetrically or asymmet- rically to allow for maintenance of the stem cell pool or become committed progenitors and differentiate into various cell lineages. The unique self-renewal capabilities and pluripotency of stem cells are integral to tissue regeneration and repair （Oh et al., 2014）. Mul- tiple mechanisms including intracellular programs and extrinsic cues are reported to regulate neural stem cell （NSC） fate （Bond et al., 2015）. A recent study, published in Cell Stern Cell, identified a novel mechanism whereby mitochondrial dynamics drive NSC fate （Khacho et al., 2016）.

关键词： ATP Regulation of neural stem cell fate decisions by mitochondrial dynamics

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How crystal configuration affects the position detection accuracy in pixelated molecular SPECT imaging systems?

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Nuclear Science and Techniques 2017年第4期28卷 24-30页

作者： Hojjat Mahani Gholamreza Raisali Alireza Kamali-asl Mohammad Reza Ay Radiation Application Research School Nuclear Science and Technology Research Institute Tehran Iran Research Center for Molecular and Cellular Imaging Tehran University of Medical Science Tehran Iran Radiation Medicine Department Shahid Beheshti UniversityTehran Iran Department of Medical Physics and Biomedical Engineering Tehran University of Medical Science Tehran Iran

It is well known that inter-crystal scattering and penetration(ICS-P) are major spatial resolution limiting parameters in dedicated SPECT scanners with pixelated *** this study,the effect of ICS-P on crystal identification in different crystal configurations was evaluated using GATE Monte Carlo simulation.A ^(99m)Tc pencil-beam toward central crystal element was *** incident angle was assumed to vary from 0° to 45° in 5° *** effects of various crystal configurations such as pixel-size,pixel-gap,and crystal material were *** influence of photon energy on the crystal identification(CI) was also *** detection accuracy(PDA) was defined as a factor indicating performance of the ***,a set of ^(99m)Tc point-source simulations was performed in order to calculate peak-to-valley(PVR) ratio for each *** results show that the CsI(Na)manifests higher PDA than NaI(TI) and YAP(Ce).In addition,as the incident angle increases,the crystal becomes less accurate in positioning of the *** a crystal-dependent critical angle,the PDA monotonically *** PDA reaches 0.44 for the CsI(Na) at 45° beam *** PDAs obtained by the point-source evaluation also behave the same as for the pencil-beam *** addition,the PVRs derived from flood images linearly correlate their corresponding *** conclusion,quantitative assessment of ICS-P is mandatory for scanner design and modeling the system matrix during iterative reconstruction algorithms for the purpose of resolution modeling in ultra-high-resolution SPECT.

关键词： Monte Carlo GATE Molecular SPECT Position detection accuracy Pixelated crystal

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QUANTITATIVE EVALUATION OF ARRANGEMENT OF MONOMERS IN LINEAR BINARY COPOLYMERS USING A MONTE CARLO SIMULATION METHOD

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Chinese Journal of Polymer Science 2009年第2期27卷 195-208页

作者： Mohammad Najafi Mehdi Salami-Kalajahi Vahid Haddadi-asl Polymer Engineering Department Amirkabir University of TechnologyP.O.Box 15875-4413TehranIran National Petrochemical Company Petrochemical Research and Technology Company14358TehranIran

A Monte Carlo method was used to take thorough account of the influences of different reactivity ratios and initial feed compositions on copolymer *** model proves the lack of azeotropic behavior in systems in which r_A>1 and r_B<1 or vice versa;it is also able to calculate the drift in the copolymer properties:copolymer composition,and randomness ***,for each reactivity ratio pair given,there is a unique reaction conversion,at which macromolecules produced inherit their ...

关键词： Radical copolymerization Copolymer microstructure Copolymer composition Monte Carlo simulation Randomness parameter Copolymer heterogeneity Azeotrope point.

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KINETIC MODELING OF ESTERIFICATION OF EPOXY RESIN IN THE PRESENCE OF TRIPHENYLPHOSPHINE FOR PRODUCING VINYL ESTER RESIN: MECHANISTIC RATE EQUATION

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Chinese Journal of Polymer Science 2006年第6期24卷 599-608页

作者： M. Rafizadeh H. Ghasemi V. Haddadi-asl Polymer Engineering Department Amirkabir University of TechnologyP. O. Box 15785-4414TehranIran

Due to its mechanical properties and ease of use, vinyl ester resin is enjoying increasing consideration. This resin normally is produced by reaction between epoxy resin and unsaturated carboxylic acid. In the present study, bis-phenol A based epoxy resin and methacrylic acid was used to produce vinyl ester resin. The reaction was conducted under both stoichiometric and non-stoichiometric conditions in the presence of triphenylphosphine as catalyst. The stoichiometric and non-stoichiometric experiments were conducted at 95, 100, 105 and 110℃ and at 90 and 95℃, respectively. The first order rate equation and mechanism based rate equation were examined. Parameters are evaluated by least square method. A comparison of mechanism based rate equation and experimental data show an excellent agreement. Finally, Arrhenius equation and activation energy were presented.

关键词： Esterification Epoxy resin Vinyl ester resin Kinetic Rate equation.

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A COMPREHENSIVE MONTE CARLO SIMULATION OF STYRENE ATOM TRANSFER RADICAL POLYMERIZATION

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Chinese Journal of Polymer Science 2010年第4期28卷 483-497页

作者： Mohammad Najafi Hossein Roghani-Mamaqani Mehdi Salami-Kalajahi Vahid Haddadi-asl International Affairs Research Institute of Petroleum Industry(RIPI)***TehranIran Polymer Engineering Department Amirkabir University of TechnologyP.O.Box 15875-4413TehranIran

An optimized and high-performance Monte Carlo simulation is developed to take thorough account of four different cases of termination in styrene ATRP. According to the simulation results, the bimolecular termination rate constant sharply drops throughout the polymerization when either chain-length dependency of termination rate constant, gel effect, or both together is applied to the simulation. In addition, as expected, the initiator is quickly decomposed at the early stages of the polymerization. The concentration of the catalyst in lower oxidation state decreases at first and then plateaus at higher conversion; furthermore, the steady concentration of Ml^nY/L in the polymerization is the highest when the chain-lengthdependent diffusion-controlled termination rate constant is employed in the simulation. The rates of deactivation and chain end degradation reactions are also smaller in this case. Therefore, the fraction of dormant chains is higher throughout the reaction and consequently the portion of dead polymers decreases. Besides, molecular weight increases linearly with conversion; however, when neither gel effect nor chain-length dependency of termination rate constant is considered, the molecular weight deviates from linearity at the end of the reaction. The peak of chain length distribution shifts toward higher molecular weight too during the reaction. Finally, the molecular weight distribution broadens at higher conversion; however, the chain length distribution of polymers produced under conditions of applying chain-length-dependent diffusion-controlled termination rate constant is narrower.

关键词： Styrene ATRP Monte Carlo simulation Chain length distribution Gel effect Chain-length-dependent termination.

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A new method for estimating the longevity and degradation of hotovoltaic systems considering weather states

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Frontiers in Energy 2016年第3期10卷 277-285页

作者： Amir AHADI Hosein HAYATI Joydeep MITRA Reza ABBASI-asl Kehinde AWODELE Young Researchers and Elite Club Ardabil Branch Islamic Azad University Ardabil *** Iran Department of Electrical and Computer Engineering Michigan State University East Lansing MI 48823 USA Department of Electrical Engineering and Computer Sciences University of California Berkeley CA 94720 USA Department of Electrical Engineering University of Cape Town Cape Town 7701 South Africa

The power output of solar photovoltaic （PV） systems is affected by solar radiation and ambient temperature. The commonly used evaluation techniques usually overlook the four weather states which are clear, cloudy, foggy, and rainy. In this paper, an ovel analytical model of the four weather conditions based on the Markov chain is proposed. The Markov method is well suited to estimate the reliability and availability of systems based on a continuous stochastic process. The proposed method is generic enough to be applied to reliability evaluation of PV systems and even other applications. Further aspects investigated include the new degradation model for reliability predication of PV modules. The results indicate that the PV module degradation over years, failures, and solar radiation must be considered in choosing an efficient PV system with an optimal design to achieve the maximum benefit of the PV system. For each aspect, a method is proposed, and the complete focusing methodology is expounded and validated using simulated point targets. The results also demonstrate the feasibility and applic- ability of the proposed method for effective modeling of the chronological aspects and stochastic characteristics of solar cells as well as the optimal configuration and sizing of large PV plants in terms of cost and reliability.

关键词： photovoltaic (PV) systems solar cell Markov model weather effects

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Celestine blue as a new indicator in electrochemical DNA biosensors

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Science China Chemistry 2016年第1期59卷 128-134页

作者： Ezat Hamidi-asl Jahan Bakhsh Raoof Abdolraoof Samadi Meibodi Zahra Haghnavaz Bazgir Eletroanalytical Chemistry Research Laboratory Department of Analytical Chemistry Faculty of Chemistry University of MazandaranBabolsarIran Spectroscopic Research Laboratory Department of Analytical ChemistryFaculty of Chemistry University of MazandaranBabolsarIran

Celestine blue(CB)was introduced as a new electroactive indicator in DNA *** interaction of CB with DNA was investigated by electrochemical and spectroscopic *** effect of buffer kind and p H on the electrochemical behavior of CB was *** peak currents of CB were linearly related to DNA concentration in the range of 5.0×10^(-9) to 1.0×10^(-7)mol/*** detection limit of this approach was 4.76×10^(-10) mol/*** on spectrometry data a hypochromic effect was observed in UV-Vis spectra of CB with increasing DNA *** results illustrate the possible interaction mode between CB and DNA is electrostatic binding.

关键词： celestine blue differential pulse voltammetry DNA biosensor electroactive indicator

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